Alright, I did some testing and think I have a clue. Steps to reproduce.
1. Deleted all the extended themes and made sure they were gone from the template_configuration table.
2. Extended a single theme.
3. Queried the template_configuration table to find new template config row.
4. In the options field, the default logo is displayed as \"brandlogofile\"

"
invalid:themes\\/survey\\/vanilla\\/files\\/logo.png\"
5. Notice where it says
invalid. Possible clue?
Moving on.
1. Upload a new image.
2. Select image using drop down and click save.
3. In the options field, the new value for brandlogofile is \"brandlogofile\"

"
invalid:image::theme::files\\\\usa_logo2.jpg\"
4. Notice where it still says
invalid.
I am no expert in LS but it looks as though the relative root path has an issue. Could be mistaken. Leaving it to you experts to decide.
Regards